EP2430441A4 - Method and system for calling variations in a sample polynucleotide sequence with respect to a reference polynucleotide sequence - Google Patents

Method and system for calling variations in a sample polynucleotide sequence with respect to a reference polynucleotide sequence

Info

Publication number
EP2430441A4
EP2430441A4 EP10770290.4A EP10770290A EP2430441A4 EP 2430441 A4 EP2430441 A4 EP 2430441A4 EP 10770290 A EP10770290 A EP 10770290A EP 2430441 A4 EP2430441 A4 EP 2430441A4
Authority
EP
European Patent Office
Prior art keywords
polynucleotide sequence
respect
sample
calling variations
calling
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Granted
Application number
EP10770290.4A
Other languages
German (de)
French (fr)
Other versions
EP2430441B1 (en
EP2430441A2 (en
Inventor
Paolo Carnevali
Jonathan M Baccash
Igor Nazarenko
Aaron L Halpern
Geoffrey Nilsen
Bruce Martin
Radoje Drmanac
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Complete Genomics Inc
Original Assignee
Complete Genomics Inc
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Complete Genomics Inc filed Critical Complete Genomics Inc
Priority to DK12165247.3T priority Critical patent/DK2511843T3/en
Priority to EP12165247.3A priority patent/EP2511843B1/en
Publication of EP2430441A2 publication Critical patent/EP2430441A2/en
Publication of EP2430441A4 publication Critical patent/EP2430441A4/en
Application granted granted Critical
Publication of EP2430441B1 publication Critical patent/EP2430441B1/en
Active legal-status Critical Current
Anticipated expiration legal-status Critical

Links

Classifications

    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/10—Ploidy or copy number detection
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/20—Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/50—Mutagenesis
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/10—Sequence alignment; Homology search
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/20—Sequence assembly

Landscapes

  • Life Sciences & Earth Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Health & Medical Sciences (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Engineering & Computer Science (AREA)
  • Biophysics (AREA)
  • General Health & Medical Sciences (AREA)
  • Analytical Chemistry (AREA)
  • Chemical & Material Sciences (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Biotechnology (AREA)
  • Evolutionary Biology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Medical Informatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • Genetics & Genomics (AREA)
  • Molecular Biology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
EP10770290.4A 2009-04-29 2010-04-28 Method and system for calling variations in a sample polynucleotide sequence with respect to a reference polynucleotide sequence Active EP2430441B1 (en)

Priority Applications (2)

Application Number Priority Date Filing Date Title
DK12165247.3T DK2511843T3 (en) 2009-04-29 2010-04-28 METHOD AND SYSTEM FOR DETERMINING VARIATIONS IN A SAMPLE POLYNUCLEOTIDE SEQUENCE IN TERMS OF A REFERENCE POLYNUCLEOTIDE SEQUENCE
EP12165247.3A EP2511843B1 (en) 2009-04-29 2010-04-28 Method and system for calling variations in a sample polynucleotide sequence with respect to a reference polynucleotide sequence

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US17396709P 2009-04-29 2009-04-29
PCT/US2010/032851 WO2010127045A2 (en) 2009-04-29 2010-04-28 Method and system for calling variations in a sample polynucleotide sequence with respect to a reference polynucleotide sequence

Related Child Applications (2)

Application Number Title Priority Date Filing Date
EP12165247.3A Division EP2511843B1 (en) 2009-04-29 2010-04-28 Method and system for calling variations in a sample polynucleotide sequence with respect to a reference polynucleotide sequence
EP12165247.3A Division-Into EP2511843B1 (en) 2009-04-29 2010-04-28 Method and system for calling variations in a sample polynucleotide sequence with respect to a reference polynucleotide sequence

Publications (3)

Publication Number Publication Date
EP2430441A2 EP2430441A2 (en) 2012-03-21
EP2430441A4 true EP2430441A4 (en) 2014-02-19
EP2430441B1 EP2430441B1 (en) 2018-06-13

Family

ID=43032762

Family Applications (2)

Application Number Title Priority Date Filing Date
EP10770290.4A Active EP2430441B1 (en) 2009-04-29 2010-04-28 Method and system for calling variations in a sample polynucleotide sequence with respect to a reference polynucleotide sequence
EP12165247.3A Active EP2511843B1 (en) 2009-04-29 2010-04-28 Method and system for calling variations in a sample polynucleotide sequence with respect to a reference polynucleotide sequence

Family Applications After (1)

Application Number Title Priority Date Filing Date
EP12165247.3A Active EP2511843B1 (en) 2009-04-29 2010-04-28 Method and system for calling variations in a sample polynucleotide sequence with respect to a reference polynucleotide sequence

Country Status (5)

Country Link
US (1) US20110004413A1 (en)
EP (2) EP2430441B1 (en)
CN (1) CN102460155B (en)
DK (1) DK2511843T3 (en)
WO (1) WO2010127045A2 (en)

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EP2511843A3 (en) 2014-02-19
CN102460155B (en) 2015-03-25
CN102460155A (en) 2012-05-16
EP2430441B1 (en) 2018-06-13
WO2010127045A2 (en) 2010-11-04
US20110004413A1 (en) 2011-01-06
DK2511843T3 (en) 2017-03-27
EP2511843B1 (en) 2016-12-21
EP2511843A2 (en) 2012-10-17
EP2430441A2 (en) 2012-03-21
WO2010127045A3 (en) 2011-01-13

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